arXiv subjects

Raymond Kapral

Publications and source records attributed to Raymond Kapral.

At least 55 records · Page 3Linked to original sources

arXiv2012

Phoretic self-propulsion: a mesoscopic description of reaction dynamics that powers motion

The fabrication of synthetic self-propelled particles and the experimental investigations of their dynamics have stimulated interest in self-generated phoretic effects that propel nano- and micron-scale objects. Theoretical modeling of these phenomena is often based on a continuum description of the solvent for different phoretic propulsion mechanisms, including, self-electrophoresis, self-diffusiophoresis and self-thermophoresis. The work in this paper considers various types of catalytic chemical reaction at the motor surface and in the bulk fluid that come into play in mesoscopic descriptions of the dynamics. The formulation is illustrated by developing the mesoscopic reaction dynamics for exothermic and dissociation reactions that are used to power motor motion. The results of simulations of the self-propelled dynamics of composite Janus particles by these mechanisms are presented.

cond-mat.soft↗

arXiv2012

Nonadiabatic Dynamics in Open Quantum-Classical Systems: Forward-Backward Trajectory Solution

A new approximate solution to the quantum-classical Liouville equation is derived starting from the formal solution of this equation in forward-backward form. The time evolution of a mixed quantum-classical system described by this equation is obtained in a coherent state basis using the mapping representation, which expresses $N$ quantum degrees of freedom in a 2N-dimensional phase space. The solution yields a simple non-Hamiltonian dynamics in which a set of $N$ coherent state coordinates evolve in forward and backward trajectories while the bath coordinates evolve under the influence of the mean potential that depends on these forward and backward trajectories. It is shown that the solution satisfies the differential form of the quantum-classical Liouville equation exactly. Relations to other mixed quantum-classical and semi-classical schemes are discussed.

physics.chem-ph↗

arXiv2012

Coarse-Grain Model for Lipid Bilayer Self-Assembly and Dynamics: Multiparticle Collision Description of the Solvent

A mesoscopic coarse-grain model for computationally-efficient simulations of biomembranes is presented. It combines molecular dynamics simulations for the lipids, modeled as elastic chains of beads, with multiparticle collision dynamics for the solvent. Self-assembly of a membrane from a uniform mixture of lipids is observed. Simulations at different temperatures demonstrate that it reproduces the gel and liquid phases of lipid bilayers. Investigations of lipid diffusion in different phases reveals a crossover from subdiffusion to normal diffusion at long times. Macroscopic membrane properties, such as stretching and bending elastic moduli, are determined directly from the mesoscopic simulations. Velocity correlation functions for membrane flows are determined and analyzed.

cond-mat.soft↗

arXiv2012

Modeling of solvent flow effects in enzyme catalysis under physiological conditions

A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with absorbing boundaries are combined with densities obtained from explicit simulation to obtain the overall probability density for the total reaction cycle time of the enzymatic system. The method is used to investigate the catalytic transfer of a phosphoryl group in a phosphoglycerate kinase-ADP-bis phosphoglycerate system, one of the steps of glycolysis. The direct simulation of the enzyme-substrate binding and reaction is carried out using an elastic network model for the protein, and the solvent motions are described by multiparticle collision dynamics, which incorporates hydrodynamic flow effects. Systems where solvent-enzyme coupling occurs through explicit intermolecular interactions, as well as systems where this coupling is taken into account by including the protein and substrate in the multiparticle collision step, are investigated and compared with simulations where hydrodynamic coupling is absent. It is demonstrated that the flow of solvent particles around the enzyme facilitates the large-scale hinge motion of the enzyme with bound substrates, and has a significant impact on the shape of the probability densities and average time scales of substrate binding for substrates near the enzyme, the closure of the enzyme after binding, and the overall time of completion of the cycle.

q-bio.BM↗

arXiv2012

Mapping quantum-classical Liouville equation: projectors and trajectories

The evolution of a mixed quantum-classical system is expressed in the mapping formalism where discrete quantum states are mapped onto oscillator states, resulting in a phase space description of the quantum degrees of freedom. By defining projection operators onto the mapping states corresponding to the physical quantum states, it is shown that the mapping quantum-classical Liouville operator commutes with the projection operator so that the dynamics is confined to the physical space. It is also shown that a trajectory-based solution of this equation can be constructed that requires the simulation of an ensemble of entangled trajectories. An approximation to this evolution equation which retains only the Poisson bracket contribution to the evolution operator does admit a solution in an ensemble of independent trajectories but it is shown that this operator does not commute with the projection operators and the dynamics may take the system outside the physical space. The dynamical instabilities, utility and domain of validity of this approximate dynamics are discussed. The effects are illustrated by simulations on several quantum systems.

physics.chem-ph↗

arXiv2010

Analysis of the quantum-classical Liouville equation in the mapping basis

The quantum-classical Liouville equation provides a description of the dynamics of a quantum subsystem coupled to a classical environment. Representing this equation in the mapping basis leads to a continuous description of discrete quantum states of the subsystem and may provide an alternate route to the construction of simulation schemes. In the mapping basis the quantum-classical Liouville equation consists of a Poisson bracket contribution and a more complex term. By transforming the evolution equation, term-by-term, back to the subsystem basis, the complex term (excess coupling term) is identified as being due to a fraction of the back reaction of the quantum subsystem on its environment. A simple approximation to quantum-classical Liouville dynamics in the mapping basis is obtained by retaining only the Poisson bracket contribution. This approximate mapping form of the quantum-classical Liouville equation can be simulated easily by Newtonian trajectories. We provide an analysis of the effects of neglecting the presence of the excess coupling term on the expectation values of various types of observables. Calculations are carried out on nonadiabatic population and quantum coherence dynamics for curve crossing models. For these observables, the effects of the excess coupling term enter indirectly in the computation and good estimates are obtained with the simplified propagation.

physics.chem-ph↗

arXiv2009

Mapping Approach for Quantum-Classical Time Correlation Functions

The calculation of quantum canonical time correlation functions is considered in this paper. Transport properties, such as diffusion and reaction rate coefficients, can be determined from time integrals of these correlation functions. Approximate, quantum-classical expressions for correlation functions, which are amenable to simulation, are derived. These expressions incorporate the full quantum equilibrium structure of the system but approximate the dynamics by quantum-classical evolution where a quantum subsystem is coupled to a classical environment. The main feature of the formulation is the use of a mapping basis where the subsystem quantum states are represented by fictitious harmonic oscillator states. This leads to a full phase space representation of the dynamics that can be simulated without appeal to surface-hopping methods. The results in this paper form the basis for new simulation algorithms for the computation of quantum transport properties of large many-body systems.

cond-mat.other↗

arXiv2009

Quantum-Classical Liouville Dynamics in the Mapping Basis

The quantum-classical Liouville equation describes the dynamics of a quantum subsystem coupled to a classical environment. It has been simulated using various methods, notably, surface-hopping schemes. A representation of this equation in the mapping Hamiltonian basis for the quantum subsystem is derived. The resulting equation of motion, in conjunction with expressions for quantum expectation values in the mapping basis, provide another route to the computation of the nonadiabatic dynamics of observables that does not involve surface-hopping dynamics. The quantum-classical Liouville equation is exact for the spin-boson system. This well-known model is simulated using an approximation to the evolution equation in the mapping basis and close agreement with exact quantum results is found.

cond-mat.other↗

arXiv2008

Surface-hopping dynamics and decoherence with quantum equilibrium structure

In open quantum systems decoherence occurs through interaction of a quantum subsystem with its environment. The computation of expectation values requires a knowledge of the quantum dynamics of operators and sampling from initial states of the density matrix describing the subsystem and bath. We consider situations where the quantum evolution can be approximated by quantum-classical Liouville dynamics and examine the circumstances under which the evolution can be reduced to surface-hopping dynamics, where the evolution consists of trajectory segments evolving exclusively on single adiabatic surfaces, with probabilistic hops between these surfaces. The justification for the reduction depends on the validity of a Markovian approximation on a bath averaged memory kernel that accounts for quantum coherence in the system. We show that such a reduction is often possible when initial sampling is from either the quantum or classical bath initial distributions. If the average is taken only over the quantum dispersion that broadens the classical distribution, then such a reduction is not always possible.

cond-mat.stat-mech↗

arXiv2007

Decoherence and Quantum-Classical Master Equation Dynamics

The conditions under which quantum-classical Liouville dynamics may be reduced to a master equation are investigated. Systems that can be partitioned into a quantum-classical subsystem interacting with a classical bath are considered. Starting with an exact non-Markovian equation for the diagonal elements of the density matrix, an evolution equation for the subsystem density matrix is derived. One contribution to this equation contains the bath average of a memory kernel that accounts for all coherences in the system. It is shown to be a rapidly decaying function, motivating a Markovian approximation on this term in the evolution equation. The resulting subsystem density matrix equation is still non-Markovian due to the fact that bath degrees of freedom have been projected out of the dynamics. Provided the computation of non-equilibrium average values or correlation functions is considered, the non-Markovian character of this equation can be removed by lifting the equation into the full phase space of the system. This leads to a trajectory description of the dynamics where each fictitious trajectory accounts for decoherence due to the bath degrees of freedom. The results are illustrated by computations of the rate constant of a model nonadiabatic chemical reaction.

cond-mat.stat-mech↗

arXiv2006

Front explosion in a periodically forced surface reaction

Resonantly-forced oscillatory reaction-diffusion systems can exhibit fronts with complicated interfacial structure separating phase-locked homogeneous states. For values of the forcing amplitude below a critical value the front "explodes" and the width of the interfacial zone grows without bound. Such front explosion phenomena are investigated for a realistic model of catalytic CO oxidation on a Pt(110) surface in the 2:1 and 3:1 resonantly-forced regimes. In the 2:1 regime, the fronts are stationary and the front explosion leads to a defect-mediated turbulent state. In the 3:1 resonantly-forced system, the fronts propagate. The front velocity tends to zero as the front explosion point is reached and the final asymptotic state is a 2:1 resonantly-locked labyrinthine pattern. The front dynamics described here should be observable in experiment since the model has been shown to capture essential features of the CO oxidation reaction.

nlin.PS↗

arXiv2004

From ballistic to Brownian vortex motion in complex oscillatory media

We show that the breaking of the rotation symmetry of spiral waves in two-dimensional complex (period-doubled or chaotic) oscillatory media by synchronization defect lines (SDL) is accompanied by an intrinsic drift of the pattern. Single vortex motion changes from ballistic flights at a well-defined angle from the SDL to Brownian-like diffusion when the turbulent character of the medium increases. It gives rise, in non-turbulent multi-spiral regimes, to a novel ``vortex liquid''.

nlin.PS↗

arXiv2004

Topological constraints on spiral wave dynamics in spherical geometries with inhomogeneous excitability

We analyze the way topological constraints and inhomogeneity in the excitability influence the dynamics of spiral waves on spheres and punctured spheres of excitable media. We generalize the definition of an index such that it characterizes not only each spiral but also each hole in punctured, oriented, compact, two-dimensional differentiable manifolds and show that the sum of the indices is conserved and zero. We also show that heterogeneity and geometry are responsible for the formation of various spiral wave attractors, in particular, pairs of spirals in which one spiral acts as a source and a second as a sink -- the latter similar to an antispiral. The results provide a basis for the analysis of the propagation of waves in heterogeneous excitable media in physical and biological systems.

nlin.PS↗

arXiv2004

Quantum-Classical Limit of Quantum Correlation Functions

A quantum-classical limit of the canonical equilibrium time correlation function for a quantum system is derived. The quantum-classical limit for the dynamics is obtained for quantum systems comprising a subsystem of light particles in a bath of heavy quantum particles. In this limit the time evolution of operators is determined by a quantum-classical Liouville operator but the full equilibrium canonical statistical description of the initial condition is retained. The quantum-classical correlation function expressions derived here provide a way to simulate the transport properties of quantum systems using quantum-classical surface-hopping dynamics combined with sampling schemes for the quantum equilibrium structure of both the subsystem of interest and its environment.

cond-mat.stat-mech↗

arXiv2003

Mesoscopic Model for Diffusion-Influenced Reaction Dynamics

A hybrid mesoscopic multi-particle collision model is used to study diffusion-influenced reaction kinetics. The mesoscopic particle dynamics conserves mass, momentum and energy so that hydrodynamic effects are fully taken into account. Reactive and non-reactive interactions with catalytic solute particles are described by full molecular dynamics. Results are presented for large-scale, three-dimensional simulations to study the influence of diffusion on the rate constants of the A+C<==>B+C reaction. In the limit of a dilute solution of catalytic C particles, the simulation results are compared with diffusion equation approaches for both the irreversible and reversible reaction cases. Simulation results for systems where the volume fraction of catalytic spheres is high are also presented, and collective interactions among reactions on catalytic spheres that introduce volume fraction dependence in the rate constants are studied.

physics.chem-ph↗

arXiv2003

Rapid convergence of time-averaged frequency in phase synchronized systems

Numerical and experimental evidence is presented to show that many phase synchronized systems of non-identical chaotic oscillators, where the chaotic state is reached through a period-doubling cascade, show rapid convergence of the time-averaged frequency. The speed of convergence toward the natural frequency scales as the inverse of the measurement period. The results also suggest an explanation for why such chaotic oscillators can be phase synchronized.

cond-mat.stat-mech↗

arXiv2003

Defect-mediated turbulence in systems with local deterministic chaos

We show that defect-mediated turbulence can exist in media where the underlying local dynamics is deterministically chaotic. While many of the characteristics of defect-mediated turbulence, such as the exponential decay of correlations and a squared Poissonian distribution for the number of defects, are identical to those seen in oscillatory media, the fluctuations in the number of defects differ significantly. The power spectra suggest the existence of underlying correlations that lead to a different and non-universal scaling structure in chaotic media.

nlin.PS↗

arXiv2002

Emergence of Quantum-Classical Dynamics in an Open Quantum Environment

The conditions under which an open quantum mechanical system may be described by mixed quantum-classical dynamics are investigated. Decoherence is studied using influence functional methods in a model composite quantum system comprising two coupled systems, A and C, interacting with a harmonic bath with Ohmic and super-Ohmic spectral densities. Subsystem A is directly coupled to subsystem C, while C is coupled directly to the bath. Calculations are presented for a model where subsystem A is taken to be a two-level system which is bilinearly coupled to a single harmonic oscillator C subsystem. The loss of quantum coherence in each subsystem is discussed in the extreme non-adiabatic regime where the dynamics of subsystem A is essentially frozen. Subsystem C is shown to lose its coherence rapidly, while subsystem A maintains coherence for longer time periods since C modulates the influence of the bath on A. Thus, one may identify situations where the coupled AC system evolution effectively obeys mixed quantum-classical dynamics.

cond-mat.mes-hall↗